Pipeline and scripts for the survey of regulatory elements and snps on coeliac disease
The repo is sub-divided into two parts analysis representing the downstream analysis of the SuRE data and pipeline respresenting the pipeline used to convert the SuRE seqeuncing data to a usable format.
analysis is likely not of much use, as this mostly contains bespoke R and bash scripts to generate and analyze the data for the manuscript
pipeline should hopefully be re-usable, but a substantial ammount of tweaking is probably required to get everything to run in your compute enviroment. Please see the wiki for a step by step walthrough of the pipeline.
pipeline_pilot contains the scripts to run the pipeline on the pilot data. This pilot is different in setup in that the genotypes are pre-defined and no genotyping is done on the data itself.
pipeline/iPCR-tools contains the java project which forms the backbone of the pipeline. This has implemented some tools that may be of use outside of only the SuRE scope.
For more details on pipeline and analysis, please see the respective folders README. Also see the wiki for a detailled walkthrough of the analysis steps.
I will likely not be maintaing this pipeline into the far future. That being said, I'll try to update the documentation the best I can and keep an eye on any issues raised here: https://github.com/OlivierBakker/CeD-SuRE-SNP/issues